Name: Paraburkholderia silvatlantica SRMrh-20
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1973

Type strain:

Species: Paraburkholderia silvatlantica

Strain Designation: SRMrh-20

Culture col. no.: DSM 21840, ATCC BAA-1244, CCUG 54297, LMG 23149, CIP 109432

Strain history: CIP <- 2006, J. Caballero-Mellado, Mexico Univ., Cuernavaca, Mexico: strain SRMrh-20

NCBI tax ID(s): 321895 (species)

SI-ID 280629

LMG 23149, ATCC BAA-1244, CCUG 54297, CIP 109432, NBRC 106337, DSM 21840

Section

Paraburkholderia silvatlantica SRMrh-20 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere ofZea mays var. Avantis.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Burkholderiaceae*
	Genus	*Paraburkholderia*
	Species	**Paraburkholderia silvatlantica**
	Full Scientific Name (LPSN)	Paraburkholderia silvatlantica (Perin et al. 2006) Sawana et al. 2015

Synonym

Burkholderia silvatlantica

Information on morphological and physiological properties Morphology

[Ref.: #31814]	Gram stain	negative
[Ref.: #122609]	Gram stain	negative

[Ref.: #31814]	Cell length	1.6-1.9 µm

[Ref.: #31814]	Cell width	0.8-0.9 µm

[Ref.: #31814]	Cell shape	rod-shaped
[Ref.: #122609]	Cell shape	rod-shaped

[Ref.: #31814]	Motility	yes
[Ref.: #122609]	Motility	yes

[Ref.: #31814]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15983]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #15983]

Culture medium growth

[Ref.: #15983]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15983]

Culture medium composition

expand / minimize

[Ref.: #15983]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #15983]

Culture medium growth

[Ref.: #15983]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15983]

Culture medium composition

expand / minimize

[Ref.: #41983]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #41983]

Culture medium growth

[Ref.: #41983]

Culture medium composition

expand / minimize

[Ref.: #122609]

Culture medium

CIP Medium 72

[Ref.: #122609]

Culture medium growth

[Ref.: #122609]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15983]	growth	30 °C
[Ref.: #31814]	growth	29-37 °C
[Ref.: #31814]	optimum	29-37 °C
[Ref.: #41983]	growth	30 °C
[Ref.: #60129]	growth	37 °C

[Ref.: #15983]	Temperature range	mesophilic
[Ref.: #31814]	Temperature range	mesophilic
[Ref.: #41983]	Temperature range	mesophilic
[Ref.: #60129]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31814]			optimum	7
[Ref.: #31814]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31814]	Oxygen tolerance	aerobe
[Ref.: #60129]	Oxygen tolerance	aerobe
[Ref.: #122609]	Oxygen tolerance	obligate aerobe

[Ref.: #31814]

Ability of spore formation

[Ref.: #31814]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #31814]	cellobiose ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	+	assimilation	* from API 20NE
[Ref.: #31814]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #31814]	nitrate ChEBI	+	reduction
[Ref.: #122609]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #122609]	nitrite ChEBI	-	reduction
[Ref.: #31814]	rhamnose ChEBI	+	carbon source
[Ref.: #31814]	ribitol ChEBI	+	carbon source
[Ref.: #31814]	ribose ChEBI	+	carbon source
[Ref.: #31814]	sucrose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122609]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #15983]	catalase	+	1.11.1.6
[Ref.: #31814]	catalase	+	1.11.1.6
[Ref.: #122609]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #31814]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[Ref.: #15983]	cytochrome-c oxidase	-	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122609]	oxidase	+/-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #31814]	urease	+	3.5.1.5
[Ref.: #122609]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #15983]	23833	+	-	-	-	-	-	-	-	+	+	+	+	+	-	+	+	+	+	+	+	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122609]	11861	-	+	+	+	-	+	+	+	-	-	+	+	-	-	-	-	+	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #15983]	Sample type/isolated from	rhizosphere ofZea mays var. Avantis
[Ref.: #15983]	Host species	Zea mays
[Ref.: #15983]	Geographic location (country and/or sea, region)	Seropédica Rio de Janeiro
[Ref.: #15983]	Country	Brazil
[Ref.: #15983]	Country ISO 3 Code	BRA
[Ref.: #15983]	Continent	Middle and South America

[Ref.: #60129]	Sample type/isolated from	Rhizosphere of maize var. Avantis A2345
[Ref.: #60129]	Geographic location (country and/or sea, region)	Rio de Janeiro,Seropédica
[Ref.: #60129]	Country	Brazil
[Ref.: #60129]	Country ISO 3 Code	BRA
[Ref.: #60129]	Continent	Middle and South America

[Ref.: #122609]	Sample type/isolated from	Environment, Maize, rhizosphere
[Ref.: #122609]	Geographic location (country and/or sea, region)	Seropedica, Rio de Janeiro
[Ref.: #122609]	Country	Brazil
[Ref.: #122609]	Country ISO 3 Code	BRA
[Ref.: #122609]	Continent	Middle and South America
[Ref.: #122609]	Isolation date	2002
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #15983]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122609]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #15983]	Burkholderia silvatlantica strain SRMrh-20 16S ribosomal RNA gene, partial sequence	AY965240	1523	ENA	686330 tax ID
[Ref.: #20218]	Burkholderia silvatlantica strain LMG 23149 16S ribosomal RNA gene, partial sequence	HQ849102	1124	ENA	321895 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paraburkholderia silvatlantica SRMrh-20	2501025504	draft	JGI IMG/M	686330 tax ID	*
[Ref.: #66792]	Paraburkholderia silvatlantica SRMrh-20	2510917014	draft	JGI IMG/M	686330 tax ID	*

Availability in culture collections External links

[Ref.: #15983]

Culture collection no.

DSM 21840, ATCC BAA-1244, CCUG 54297, LMG 23149, CIP 109432

[Ref.: #71618]

SI-ID 280629

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paraburkholderia caseinilytica sp. nov., isolated from the pine and broad-leaf mixed forest soil.	Gao ZH, Zhong SF, Lu ZE, Xiao SY, Qiu LH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002774	2018	*
Phylogeny	Burkholderia silvatlantica sp. nov., a diazotrophic bacterium associated with sugar cane and maize.	Perin L, Martinez-Aguilar L, Paredes-Valdez G, Baldani JI, Estrada-de Los Santos P, Reis VM, Caballero-Mellado J	Int J Syst Evol Microbiol	10.1099/ijs.0.64362-0	2006	*

References

#15983

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21840

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#31814

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28082 (see below)

#41983 ; Curators of the CIP;
#60129 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54297

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#68369

Automatically annotated from API 20NE .

#68382

Automatically annotated from API zym .

#71618

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID280629.1 )

#122609 Collection of Institut Pasteur ; Curators of the CIP; CIP 109432

#28082

IJSEM 1931 2006 ( DOI 10.1099/ijs.0.64362-0 , PubMed 16902033 )

* These data were automatically processed and therefore are not curated

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